Orchard and storage-dependent metabolic and transcriptional regulation of superficial scald in ‘Packham’s Triumph’ pears

Superficial scald (SS), a chilling-induced peel disorder, limits the storability and marketability of cold-stored ‘Packham’s Triumph’ pears. This study combined gene expression and non-polar metabolomic profiling to elucidate orchard- and storage-specific mechanisms regulating SS development. Pears were sourced from three commercial orchards and stored under regular atmosphere (RA), controlled atmosphere (CA), or stepwise cooling (SWC). Controlled atmosphere (CA) consistently provided the greatest suppression of SS, whereas the effectiveness of stepwise cooling (SWC) varied among orchards. Gene expression analysis showed that storage atmosphere regulated stress- and senescence-related genes, with antioxidant-associated genes (GST and GPx) generally enhanced under CA and SWC, while lipid degradation- and senescence-associated genes (LPS, LOX, and SGR) exhibited storage- and orchard-dependent responses. Metabolomic analyses revealed coordinated changes in farnesyl conjugates, hydroxycinnamoyl acyl esters, diacylglycerols, triacylglycerols, phytosterol conjugates, and sphingolipids under scald-suppressive storage conditions. Correlation network analysis further identified coordinated associations between stress-responsive genes, particularly 9-cis-epoxycarotenoid dioxygenase (NCED), and metabolites involved in membrane lipid remodeling and secondary metabolism. These findings improve our understanding of the molecular basis of superficial scald in pear and identify candidate gene and metabolite biomarkers that could support orchard-specific scald risk assessment and the development of targeted postharvest storage strategies.